Module 3: Sequence Alignment

Module topics

  • Introduction to searching and sequence alignment
  • Pairwise sequence alignment
  • BLAST algorithm


SessionLecture RecordingsLecture SlidesPractical Assignment 
10. Introduction_Jonathan Kayondo
1. Module3_Session1_Part1
2. Module3_Session1_Part2
3. Module3_Session1_Part3
4. Module3_Session1_Part4
5. Module3_Session1_Part5
6. Module3_Practical
Module3_Session1Module 3_Session.1_pracUPDATED

Module 3_Session.1_pracUPDATED._pdf
21. Module3_Session2_Part1
2. Module3_Session2_Part2
3. Module3_Session2_Part3
4. Module3_Session2_Part4
5. Module3_Session2_Part5


30. Sonal - Meet the trainer
1. Module3_Session.3_part.1
2. Module3_Session3_part2
3. Module3_Session3_part3
4. Module3_Session3_part4
5. Module3_Session3_part5-prac
Module3_Session.3Module 3_Session.3_prac




Jonathan Kayondo


Affiliation: Uganda Virus Research Institute

I am a Senior Research Officer (SRO) at the Uganda Virus Research Institute (UVRI), with a molecular genetic training background. My research encompasses investigations on disease vectors and pathogens with a focus on the genetics of malaria transmitting mosquitoes and HIV drug resistance. I am currently involved in research exploring controlling malaria vectors using engineered endonucleases, and the design of more sensitive assays for detection of HIV-drug resistance minority variants. I also contribute to Bioinformatics capacity development at the institute where various analysis pipelines, e.g. for NGS-based metagenomics and variant calling, are being developed to enhance pathogen detection for research purposes or disease outbreak investigations. The Uganda Virus Research Institute is a reference centre for various viral infections and is involved in investigations on communicable and also non-communicable diseases to generate information that will help initiate new or to improve on existing control and prevention strategies.



Sonal Henson


Affiliation: International Centre of Insect Physiology and Ecology

I have recently joined ICIPE as a postdoctoral Bioinformatician. My interest in Bioinformatics started from my undergraduate course in Computational Biology at the University of Warwick, UK. I followed it by obtaining an MSc in Bioinformatics from University of Leicester, UK. I was awarded a PhD by University of Pretoria for research I carried out on the transcriptome and the genome of the Brown ear tick, the primary vector for East Coast Fever (ECF) disease in cattle. This work was done at the International Livestock Research Institute (ILRI). For my first postdoc, for which I was based at ILRI and Functional Genomics Centre, Zurich, I studied the genomes of Theileria parva, the protozoan causing ECF. After that I moved to studying the genomes of pathogenic bacteria and viruses at the KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya. More recently I have been involved in a project to characterise MHC class I alleles from African pigs.